Fellas,
I run the M&K dual outlet exhaust as seen here. I have not added a factory airbox, yet. My engine is spaced about 1/2" down for more clearance. I did create a bubble in the rear parcel shelf for clearance, yet the top of the rubber air intake touches the parcel shelf. The top for me, is a rubber hoop which retains the IAC motor.
Scott, does the factory air filter housing sit higher than the rubber elbow which is between the throttle and the intake manifold? If so, then I think clearance may be an issue.